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A rapid micro chromatin immunoprecipitation assay (ChIP)

Nature Protocols volume 3, pages 10321045 (2008) | Download Citation

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Abstract

Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein–DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (μChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. μChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make μChIP applicable to 1-mm3 fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes 8 h for 16 ChIPs.

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Acknowledgements

This work is supported by the FUGE, YFF, STAMCELLE and STORFORSK programs of the Research Council of Norway and by the Norwegian Cancer Society.

Author information

Affiliations

  1. Department of Biochemistry, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo 0317, Norway.

    • John Arne Dahl
    •  & Philippe Collas

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  1. Search for John Arne Dahl in:

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Competing interests

Philippe Collas is a consultant for Diagenode SA, Liege, Belgium

Corresponding author

Correspondence to Philippe Collas.

Supplementary information

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  1. 1.

    Supplementary Figure 1

    Real-time PCR profiles after analysis of DNA from a 100,000-cell ChIP and of a 100-cell ChIP

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DOI

https://doi.org/10.1038/nprot.2008.68

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